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  • Polymer and Materials Science  (6,093)
  • Chemical Engineering  (1,134)
  • 1980-1984  (7,227)
  • 1970-1974
  • 1930-1934
  • 1925-1929
  • 1984  (3,658)
  • 1983  (3,569)
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  • 1980-1984  (7,227)
  • 1970-1974
  • 1930-1934
  • 1925-1929
Year
  • 101
    Electronic Resource
    Electronic Resource
    An analysis of the sequence dependence of the structure and energy of A- and B-DNA models using molecular mechannics (1983)
    New York : Wiley-Blackwell
    Biopolymers 22 (1983), S. 969-1002 
    Details
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Molecular-mechanics calculations have been carried out on the base-paired hexanucleoside pentaphosphates d(TATATA)2, d(ATATAT)2, d(A6)·d(T6), d(CGCGCG)2, d(GCGCGC)2, and d(C6)·d(G6) in both A- and B-DNA geometries. The calculated relative energies of these polymers are consistent with the relative stabilities of the polymers found experimentally. In particular, the results of our calculations support the observation that the homopolymer d(A)n·d(T)n is more stable in a B-DNA conformation, while the homopolymer d(G)n·d(C)n is more stable in an A-DNA conformation. The molecular interactions responsible for these differential stabilities include both inter- and intrastrand base stacking, as well as base-phosphate interactions. While definitive experiments on the heteropolymer stabilities have not yet been carried out, the results of our calculations also suggest a greater stability of the purine-3′,5′-pyrimidine sequence over the pyrimidine-3′,5′-purine sequence in both the A- and B-conformations. The reason for this greater stability lies in the importance of the inherent directionality (5′ → 3′ vs 3′ → 5′) of phosphate-base and base-base interactions. The largest conformation change observed on energy refinement is sugar repuckering, which occurs mainly on pyrimidine-attched sugars and only in the B-DNA geometry. We suggest a molecular mechanism, specifically, differential base-sugar steric interactions involving neighboring sugars, to explain why this repuckering occurs more with d(A6)·d(T6) than with other isomers.
    Additional Material: 10 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/bip.360220316
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  • 102
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    Salt- and sequence-dependence of the secondary structure of DNA in Solution by 31P-nmr spectroscopy (1983)
    New York : Wiley-Blackwell
    Biopolymers 22 (1983), S. 879-893 
    Details
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: We examined three sonicated, specific-seqiemce polydeoxynucleotides in solution over a wide range of concentrations of several salts by 13P-nmr spectroscopy, and we found that the alternating copolymer poly(dAdT)·poly(dAdT) exhibits a dinucleotide repeat unit in all five salts and at all concentrations studied, as indicated by the presence of a doubled in its 31P-nmr spectra. The two components of the doublet show selective shift effects. The upfield component is assigned to dApdT in the gauche--gauche- conformation and shifts upfield in all four monovalent salts used, relative to a single-stranded oligonucleotide control. The downfield component is assigned to dTpdA in the trans-gauche- conformation and shifts downfield with increasing CsF concentration but remains essentially constant in LiCl, NaCl, and CsCl. These changes indicate a fast noncooperative transition for poly(dAdT)·poly-(dAdT) from a presumed right-handed dinucleotide-repeat B-form to another conformation with a dinucleotide-repeat structure, via a continuum of structures that may differ in the extent of the winding of the double helix. Ethanol causes the upfield component to collapse into the other component, indicating conversion to a structure with a mononucleotide repeat unit and a trans-gauche- conformation. Up to 1M Mg2+ appears to have no significant effect on the phosphodiester conformations of poly(dAdT)·poly(dAdT). By contrast, poly-(dGdC)·poly(dGdC) gives a slow cooperative transition from what is considered to be a right-handed regular B-form to a left-handed Z-form on increasing MgCl2 and NaCl concentrations, although we observed no changes in chemical shifts below the transition points. The homopolymer poly(dA)·poly(dT) exhibits no unusual shift effects or transitions upon the addition of salts when compared to the oligonucleotide control and is considered to be a regular B-form with a gauche--gauche- phosphodiester backbone conformation. These differences emphasize the distinct secondary structures of DNAs of different sequences and their selective responses to changes in solution conditions.
    Additional Material: 7 Ill.
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    URL: http://dx.doi.org/10.1002/bip.360220310
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  • 103
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    1H-nmr studies on the dinucleoside monophosphates containing 2′-halogeno-2′-deoxypurinenucleosides: Effects of 2′-substitutes on conformation (1983)
    New York : Wiley-Blackwell
    Biopolymers 22 (1983), S. 1189-1202 
    Details
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Seven dinucleoside monophosphates containing 2′-halogeno-2′-deoxypurine nucleoside residue, dAfl-U, dAcl-U, dAbr-U, dAio-U, dGfl-U, and dIfl-C, were chemically synthesized and investigated by 1H-nmr spectroscopy at 300 MHz. The sugar and backbone conformations of these compounds were analyzed by the spectral pattern of furanose proton resonances; and the extents of base-base interaction were estimated from chemical shifts and their temperature-dependent changes of base-proton resonances. It is found that the population of C3′-endo conformer and the extent of base-base interaction decrease as the electronegativity of 2′-substituent decreases in dAx-U (x = fl, cl, br, and io) series. The C3′-endo (3E) population and the base-base interaction in Nfl-U (N = A,G)-type dimers as well as dIfl-C are relatively higher than the corresponding natural ribo-dimers but can be recognized as grossly similar to the conformation of regular RNA dimers.
    Additional Material: 3 Ill.
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    URL: http://dx.doi.org/10.1002/bip.360220412
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  • 104
    Electronic Resource
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    Masthead (1983)
    New York : Wiley-Blackwell
    Biopolymers 22 (1983) 
    Details
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/bip.360220501
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  • 105
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    Raman spectra and normal vibrations of dipeptides. I. Glycylglycine (1983)
    New York : Wiley-Blackwell
    Biopolymers 22 (1983), S. 1267-1283 
    Details
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: We studied the Raman spectra of the zwitterionic glycylglycine crystal (GG) and its N-deuterated analog. A normal coordinate analysis on its α-crystalline form was performed and the effects of intra-and intermolecular couplings are discussed. A modified Urey-Bradley potential was used as a model of the intramolecular force field. Factor group splittings are described by the use of intermolecular potentials consisting of nonbonded atom-atom interactions and dipole-dipole interactions. Effects of hydrogen bonds on the vibrational frequencies of amino and carboxylate groups are also analyzed.
    Additional Material: 9 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/bip.360220503
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  • 106
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    Peptaibol antibiotics: Conformational preferences of synthetic emerimicin fragmentsThis is part 90 of the Linear Oligopeptides series. For part 89, see Toniolo, C., Bonora, G. M., Anzinger, H. & Mutter, M. (1982) Macromolecules (in press). (1983)
    New York : Wiley-Blackwell
    Biopolymers 22 (1983), S. 1335-1356 
    Details
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The ir absorption and CD conformational analyses of solutions of the protected 2-9 fragment of the peptaibol antibiotics emerimicins III and IV \documentclass{article}\pagestyle{empty}\begin{document}$ \rlap{--} (Aib_3 \rlap{--} )L - Val - Gly - L - Leu\rlap{--} (Aib_2 \rlap{--} ) $\end{document} and related short sequences are consistent with the presence of a right-handed α-helix for the octapeptide, while the tri-, tetra-, and pentapeptides adopt a 310-helix, either right- or left-handed, depending on the amino acid sequences. The structural preferences of solid-state \documentclass{article}\pagestyle{empty}\begin{document}$ Z\rlap{--} (Aib_3 \rlap{--} )L - Val - OMe $\end{document} and \documentclass{article}\pagestyle{empty}\begin{document}$ Z\rlap{--} (Aib_3 \rlap{--} )L - Val - Gly - OMe $\end{document} have been determined by x-ray diffraction. In accord with the solution data, incipient 310-helices, formed by two and three β-turns, have been found for the tetra- and pentapeptides, respectively. The tetrapeptide helix has the left-handed screw sense, while that of the pentapetide is right-handed, thus confirming the conclusions of the CD analysis of the solution.
    Additional Material: 3 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/bip.360220507
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  • 107
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    Mobility of oligopeptides on normal-phase silica: Effect of positional isomerism (1983)
    New York : Wiley-Blackwell
    Biopolymers 22 (1983), S. 1401-1407 
    Details
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Isomeric oligopeptides composed of five methionyl residues and one glycyl residue or of five γ-methyl-L-glutamyl residues and one glycyl residue all exhibit marked differences in retention on normal-phase silica. When the glycyl residue is at internal positions of hexa or heptapeptides, the peptide elutes most rapidly form the μPorasil column. Comparison of the effect of positional isomerism on retention in short oligopeptides with the effect on retention of hexamers and heptamers suggests that a change in peptide conformation may be responsible for the change in oligopeptide mobility.
    Additional Material: 3 Ill.
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    URL: http://dx.doi.org/10.1002/bip.360220511
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  • 108
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    Vacuum-ultraviolet circular dichroism of sodium hyaluronate oligosaccharides and polymer segments (1983)
    New York : Wiley-Blackwell
    Biopolymers 22 (1983), S. 1319-1334 
    Details
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The CD spectrum of an enzymatically derived sodium hyaluronate (NaHA) segment preparation with chain length 18 ± 3 disaccharide units [NaHAseg, ( NaGlcUA GlcNAc)15-20°. NaGlcUA, sodium D-glucuronate; GlcNAc, 2-acetamido-2-deoxy-D-glucose] in H2O was recorded to 180 nm using a computer-controlled vacuum-uv CD instrument. Near 190 nm the spectrum is of low intensity, similar to the sum of the free monosaccharide contributios, attributed to the π-π* transitions of the acetamido and carboxylate substituents. In contrast, much smaller oligosaccharides, also derived from high-molecular-weight NaHA by enzymatic digestions, show CD spectra in H2O with prominent bands centered near 190 nm. The oligosaccharide spectra can be matched as linear combinations of interior sugar residue (= NaHAseg) and end sugar residue CD contributions. End residues from oligosaccharides of the type (NaGlcUA-GlcNAc)n show a negative CD band near 190 nm. End residues from oligosaccharides of the reverse sequence (GlcNAc-NaGlcUA)n show a positive CD band near 190 nm. Averaging of the two end-residue spectral contributions yields an approximate match for the spectrum of NAHAseg below 200 nm. It is proposed that the low intensity CD of NaHA in the π-π* region is the result of large-magnitude, oppositely signed contributions, which can be visulized by studying oligosaccharides.
    Additional Material: 6 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/bip.360220506
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  • 109
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    Structure of a cellulose II-hydrazine complex (1983)
    New York : Wiley-Blackwell
    Biopolymers 22 (1983), S. 1383-1399 
    Details
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The structure of a crystalline cellulose II-hydrazine complex has been determined by x-ray diffraction methods as part of an investigation of cellulose-solvent interaction. The complex studied was that formed when Fortisan fibers were swollen in hydrazine and then vacuumdried. The unit cell is monoclinic with dimensions a = 9.37 Å, b = 19.88 Å, c = 10.39 Å, and γ = 120.0° and contains disaccharide segments of four chains, with one hydrazine per glucose residue. In view of the limited x-ray intensity data, the structure has been determined based on an approximate unit cell containing two chain segments, with a = 4.69 Å, using the linked-atom least-squares refinement procedures. The refined model contains antiparallel cellulose chains that are linked by both intermolecular hydrogen bonds and hydrogen-bonded hydrazine molecules. The parallel chains in the 020 planes are packed in register, leading to stacks of chains analogous to those in chitin. All the hydroxyl groups are satisfactorily hydrogen-bonded, and each hydrazine forms four donor and two acceptor hydrogen bonds, including an N—H…N bond between hydrazines. From this work it can be seen that the interaction of cellulose II with hydrazine involves scission of the intermolecular hydrogen bonds followed by disruption of the stacks of quarter-staggered chains. The latter effect is probably necessary for hydrazine to act as a cellulose solvent.
    Additional Material: 6 Ill.
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    URL: http://dx.doi.org/10.1002/bip.360220510
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  • 110
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    Vacuum ultraviolet circular dichroism of poly(dI-dC)·poly(dI-dC): No evidence for a left-handed double helix (1983)
    New York : Wiley-Blackwell
    Biopolymers 22 (1983), S. 1445-1448 
    Details
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Additional Material: 1 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/bip.360220602
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  • 111
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    Conformational analysis of acetyl-L-phenylalanine p-acetyl and p-valeryl anilides (1983)
    New York : Wiley-Blackwell
    Biopolymers 22 (1983), S. 1489-1498 
    Details
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Empirical force-field calculations and ir and 1H-nmr spectra indicate that five-membered (C5) and seven-membered (C7eq) hydrogen-bonded rings are the preferred conformations of acetyl-L-Phe p-acetyl and p-valeryl anilides in nonpolar media. The C5/C7eq ratio was found to be dependent on the dryness of the solute and the solvent. This fact and the results from conformational-energy calculations suggest that a molecule of water participates in the stabilization of the C7eq conformation.
    Additional Material: 4 Ill.
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    URL: http://dx.doi.org/10.1002/bip.360220605
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  • 112
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    X-ray diffraction study of the interaction of the amino terminal half-molecule of histone H4 with duplex DNA (1983)
    New York : Wiley-Blackwell
    Biopolymers 22 (1983), S. 333-339 
    Details
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The interaction of the amino terminal half-molecule of histone H4 with duplex DNA has been studied by fiber x-ray diffraction. Changes induced in the diffraction pattern of B-DNA by the presence of the bound peptide have been Fourier-analyzed and the results presented in terms of a deweighted radial projection of the electron density. We conclude that the peptide binds on the major groove side of the sugar-phosphate chain.
    Additional Material: 3 Ill.
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    URL: http://dx.doi.org/10.1002/bip.360220143
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  • 113
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    Neurophysin-neuropeptide hormone complexes: Biosynthetic origin and noncovalent interactions (1983)
    New York : Wiley-Blackwell
    Biopolymers 22 (1983), S. 355-362 
    Details
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Recent studies of the neurophysins and associated neuropeptide hormones have addressed both the biosynthetic pathways by which these noncovalent protein-peptide complexes are derived in neurosecretory neurons and the nature of the noncovalent interactions likely to occur during transport and storage in neurosecretory granules within the neurons. In vitro translation of hypothalamic mRNA and sequencing of cDNA obtained from this mRNA have yielded chemical evidence that each complex of hormone and major neurophysin is made through a common precursor molecule. The mature complexes obtained upon proteolytic processing of precursors exhibit interdependent hormone binding and self-association interactions. Photoaffinity labeling and quantitative affinity chromatography have helped detect and define the binding surfaces involved. Further study of the structural nature of these surfaces is being carried out using large neurophysin fragments obtained by limited tryptic proteolysis.
    Additional Material: 4 Ill.
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    URL: http://dx.doi.org/10.1002/bip.360220146
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  • 114
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    Gramicidin a adopts distinctly different conformations in membranes and in organic solvents (1983)
    New York : Wiley-Blackwell
    Biopolymers 22 (1983), S. 397-402 
    Details
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Gramicidin A exists in distinctly different conformations in phospholipid vesicles and in organic solvents. These different folding motifs are also reflected in crystals of gramicidin formed in the presence and absence of lipid molecules.
    Additional Material: 3 Ill.
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    URL: http://dx.doi.org/10.1002/bip.360220152
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  • 115
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    Design, synthesis, and conformation of ion carriers (1983)
    New York : Wiley-Blackwell
    Biopolymers 22 (1983), S. 409-414 
    Details
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Macrocyclic molecules can serve as ion carriers when their polar groups form an inner cage to capture ions while their hydrophobic groups form an outer layer to dissolve the molecule in lipid membranes. A “template method” has been developed for high-yield synthesis of a whole variety of macrocyclic esters, amides, and other families which may show ionophoric properties. In order to select the more promising compounds for synthesis, energetic and conformational characteristics of such molecules have been calculated from empirical energy functions. Calculations are examined using known structures and are employed to predict the properties of molecules not yet synthesized.
    Additional Material: 2 Ill.
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    URL: http://dx.doi.org/10.1002/bip.360220154
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  • 116
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    The T-cell receptor as analyzed by functional T-cell lines specific to a synthetic polypeptide antigen (1983)
    New York : Wiley-Blackwell
    Biopolymers 22 (1983), S. 453-464 
    Details
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: For a better understanding of the molecular nature of the antigen-specific T-cell recognition system, continuous T-cell lines specific to the synthetic polypeptide antigen poly(Tyr,Glu)-poly(DLAla)--poly(Lys) [(T,G)-A--L] were established from C3H.SW (high-responder) activated T-cells, cloned, and characterized. These lines and their derived clones are also constitutive secretors of antigen-specific T-cell replacing helper factors. The secreted T-cell helper factor was shown to possess MHC determinants as well as V-region determinants, or more specifically, idiotypic determinants that are cross-reactive with those expressed on (T,G)-A--L-specific antibodies of the same mouse strain. Using the fluorescence-activated cell sorter (FACS II) and individual C57BL/6 anti-idiotypic sera produced against (T,G)-A--L-specific antibodies of C3H.SW origin, we have demonstrated the expression of the cross-reactive idiotypic markers on the monoclonal helper T-cells. Attempts were made to purify the active fraction of the T-cell factors secreted by the (T,G)-A--L continuous helper lines. Gel analysis of the twice affinity-purified eluate of a (T,G)-A--L column revealed the existence of iodinated bands with molecular weight of 17,000 and 15,000, in addition to a diffuse band of high molecular weight. The specific helper activity of the factors was associated with a 65-75% ammonium sulfate precipitate. Gel electrophoresis of the latter fraction, as well as of an eluate of a (T,G)-A--L-Sepharose column indicated that a high-molecular-weight (〈 67,000) and a low-molecular-weight (15,000-17,000) fraction contained the biological activity of the factor. Similar results were obtained following chromatography of the factor on Sephadex G-100 columns. The two fractions were shown to be synthesized by the T-cell lines, as indicated by internal labeling experiments using 35S-methionine. Thus, it is suggested that a fraction of an apparent molecular weight of 15,000-17,000 preserves both the antigen specificity and the helper activity of the factor produced by the (T,G)-A--L-specific T-cell lines.
    Additional Material: 6 Ill.
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    URL: http://dx.doi.org/10.1002/bip.360220158
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  • 117
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    β-Galactosidase: Immune recognition of conformation and mechanism of antibody-induced catalytic activation (1983)
    New York : Wiley-Blackwell
    Biopolymers 22 (1983), S. 465-473 
    Details
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Activation of mutant β-galactosidase by antibodies can be explained by a “selection” mechanism in which the antibody binds and stabilizes those mutants in a native-like conformation and by an “induction” mechanism where binding of the antibody itself induces a conformational change activating β-galactosidase. The “selection” hypothesis was tested by passing β-galactosidase through a column packed with monoclonal antibody-derivatized Sepharose. The antibody retains the active, in preference to the inactive, proteins. The “induction” mechanism was tested by mixing antibody-Sepharose with mutant β-galactosidase and measuring enzyme activity before mixing and that remaining in the supernatant. The activity of the antibody-Sepharose pellet exceeded the sum of the original activity plus supernatant activity. As a result of these experiments, both mechanisms are found to be operative.
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    URL: http://dx.doi.org/10.1002/bip.360220159
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  • 118
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    Exploitation and exploration of ceruletide and eledoisin, two peptides of nonmammalian origin (1983)
    New York : Wiley-Blackwell
    Biopolymers 22 (1983), S. 507-515 
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    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Eledoisin and ceruletide, two nonmammalian hormonelike peptides, have been explored for possible pharmaceutical application. At present, only a few of the potentialities of the two drugs have been exploited. Eledoisin is used in ophthalmology as a lachrymal secretagogue; ceruletide is applied in the radiological diagnosis of gallbladder, biliary system, and digestive tract disorders, in the study of exocrine pancreatic function, and in the treatment of postoperative paralytic ileus and intestinal hypotony and atony. Possible analgesic and antipsychotic applications of ceruletide are under study. Developments of synthetic and analytical methods for both peptides are briefly reviewed. Technical devices or alternative routes of administration are envisaged in order to enlarge both the present market and the field of application.
    Additional Material: 4 Ill.
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    URL: http://dx.doi.org/10.1002/bip.360220164
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  • 119
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    Proton NMR studies of partially modified retro-inverso peptides (1983)
    New York : Wiley-Blackwell
    Biopolymers 22 (1983), S. 1869-1883 
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    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: High-resolution 1H-nmr analyses are presented for partially modified retro-inverso derivatives of peptides with emphasis on enkephalins. Studies in DMSO-d6 reveal the unique as well as common characteristics of the non-amino acid residues incorporated into these modified peptides. The complete assignment of 1,1-diaminoalkyl and malonyl, as well as of amino acid, residues provides the basis for the exploration of the conformational features induced in peptides by such topochemical modifications.
    Additional Material: 3 Ill.
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    URL: http://dx.doi.org/10.1002/bip.360220805
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  • 120
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    Fluorescence correlation spectroscopy and photobleaching recovery of multiple binding reactions. II. FPR and FCS measurements at low and high DNA concentrations (1983)
    New York : Wiley-Blackwell
    Biopolymers 22 (1983), S. 1949-1966 
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    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The preceding paper develops the theory for the interpretation of fluorescence photobleaching recovery (FPR) measurements of multiple binding of a ligand to a multivalent substrate molecule. Based on a reasonable assumption about the mechanism of the photobleaching process, this analysis shows that the observed behavior of a multivalent system should be practically identical to that of a univalent binding system. This is in contrast to the expected and observed behavior of fluorescence correlation spectroscopy (FCS) measurments. Experimental FPR measurements of multivalent binding of ethidium bromide to DNA confirm these conclusions. The FCS and FPR measurements also reveal an apparently enhanced diffusion of ethidium at high DNA concentration. This enhancement might result from direct transfer of ethidium among DNA molecules.
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    URL: http://dx.doi.org/10.1002/bip.360220809
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    Correlation of Tm, sequence, and ΔH of complementary RNA helices and comparison with DNA helices (1983)
    New York : Wiley-Blackwell
    Biopolymers 22 (1983), S. 2001-2016 
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    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Tm values of 16 fully complementary RNA duplexes with repeating base sequence have been employed as the empirical basis for developing a reliable and practical method for computing apparent enthalpies (ΔHcalc) for their helix → coil transitions. The approach taken is the same as in the accompanying investigation of DNA duplexes, although some of the computational variables of the “best-fit” function are necessarily different due to the distinguishing structural properties of the RNA-type helix. An excellent linear correlation was thus obtained between experimental Tm and ΔHcalc values. An equally good fit was obtained between Tm and ΔHcalc for five unrelated (to the 16 RNAs) decaribonucleotide duplexes. The differences in computational variables between the best-fit methods for RNA and DNA duplexes are shown to be a reflection of differences in cation binding and the effective local dielectric. The greater Tm dependence on G·C content of RNA helices than of DNA helices is shown to be due to a greater latitude of stacking stabilities of complementary dinucleotide fragments containing A·T than A·U base pairs.
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    Possible observation of a defect resonance in DNA (1983)
    New York : Wiley-Blackwell
    Biopolymers 22 (1983), S. 2045-2060 
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    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: A sharp feature is observed at about 600 MHz in the inelastic scattered light spectrum of fibers of calf thymus DNA. It broadens so as to be no longer distinctly resolved when the ordering of a fiber is disrupted by convection caused by laser heating. To within experimental uncertainties the frequency of this feature is wavevector independent. A possible origin of the feature lies in a defect resonance such as that associated with the chain terminus.
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    Infrared spectroscopic study of C7 intramolecular hydrogen bonds in peptidesContribution No. 156 from the Solid State and Structural Chemistry Unit. (1983)
    New York : Wiley-Blackwell
    Biopolymers 22 (1983), S. 2091-2104 
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    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The ir-spectra in the N—H stretching region of Piv-Pro-NHMe and Boc-Pro-NHMe have been studied in carbon tetrachloride and chloroform solutions over a wide range of concentrations. Based on the concentration dependence of the N—H stretching bands, it has been shown that the characteristic N—H stretching band due to the C7 intramolecular hydrogen bond is around 3335 cm-1. Intermolecular hydrogen bonding also occurs to a small extent in these peptides, giving rise to a slight concentration dependence of the N—H stretching bands. The band around 3335 cm-1 need not necessarily be due to C7 hydrogen bonds alone as proposed by Tsuboi et al. or to intermolecular hydrogen bonding alone as proposed by Maxfield et al.; this conclusion is supported by studies on Boc-Leu-NHMe, which undergoes only intermolecular hydrogen bonding. We have shown that Z-Aib-Aib-OMe and Z-Aib-Ala-OMe form C7 intramolecular hydrogen bonds in addition to C5 intramolecular hydrogen bonds. The present studies also show that all the peptides studied exist in more than one conformation in solution.
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    Comparison of analytically and numerically derived hydrogen exchange-rate distribution functions (1983)
    New York : Wiley-Blackwell
    Biopolymers 22 (1983), S. 895-909 
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    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Hydrogen exchange-rate probability density functions for lysozyme have been derived by numerical Laplace inversion with the computer program CONTIN. The resulting solution set includes a smooth bimodal solution in agreement with previous analytical results together with a smooth three-peak solution. Numerical analysis of lysozyme hydrogen-exchange data in glycerol/water cosolvent mixtures confirms the previous assignment of the slow-exchange peak to an exchange mechanism involving reversible unfolding. Physicochemical constrations that can reduce the size of the solution set are described. The results are compared with those obtained from previous analytical methods and the limitations of the discrete class and analytical appraches are discussed.
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    High-resolution nmr studies of A- and G-containing oligonucleotides (1983)
    New York : Wiley-Blackwell
    Biopolymers 22 (1983), S. 919-933 
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    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: We report the temperature dependence of the H2 and H8 purine ring proton resonances of oligoriboadenylates up to chain length 11, with or without a single guanosine residue at the 5′-end, second position, or 3′-end. The results suggest the following generalizations: (1) Stacking of the bases in a right-handed single-stranded helix is more extensive in the interior of the chain than at the chain ends. (2) The tendency of the terminal base to unstack is greater at the 5′-end than at the 3′-terminus. (3) G stacks more weakly than A, as evidenced by weak stacking of 3′-terminal G. Anomalies were also observed in the unstacking profile of G at the second position in the chain, indicating a conformational anomaly such as looping out of G, thereby allowing adjacent A's to stack together, or adoption by G of some other alternative structure. (4) The results imply that the environment at a given base is influenced by effects of longer range than nearest- or next-nearest-neighbor. Increasing ion condensation as chain length increases may be responsible for the slow approach of oligomer behavior to the properties of the high polymer.
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    Masthead (1983)
    New York : Wiley-Blackwell
    Biopolymers 22 (1983) 
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    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
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    URL: http://dx.doi.org/10.1002/bip.360220401
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    Collapse of DNA caused by trivalent cations: pH and ionic specificity effects (1983)
    New York : Wiley-Blackwell
    Biopolymers 22 (1983), S. 1097-1106 
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    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: A comparison of the condensation of T4 phage DNA by spermidine and Co(NH3)63+ at pH values between 5.1 and 10.2 has been made using quasielastic light scattering to determine translational diffusion coefficients and Stokes radii. Co(NH3)63+ is more effective than spermidine in causing condensation at all pH, indicating that the differences observed in previous work were not due to pH effects, as might have been inferred from recent theories of intermolecular forces. The DNA particles collapsed with Co(NH3)63+ are smaller than those obtained with spermidine. The hydrodynamic radius of spermide-collapsed structures decreases slightly with increasing pH, while the size of the Co(NH3)63+collapsed structures is almost independent of pH. These results confirm that there are specific ion effects in DNA condensation by oligocations, in addition to the dominant general polyelectrolyte effects.
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    Nuclear magnetic resonance study of ring conformations of cyclic tetradepsipeptide AM-toxins and related peptides (1983)
    New York : Wiley-Blackwell
    Biopolymers 22 (1983), S. 1167-1187 
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    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Cyclic tetradepsipeptides, AM-toxin I and II, are the host-specific phytotoxins of Alternaria mali. In order to elucidate conformation-toxicity relationships, we analyzed the 270-MHz proton nmr spectra of AM-toxins and hydrogenated analogs, (D-Ala2)AM-toxin I (toxic) and (L-Ala2)AM-toxin I (not toxic), in (C2H3)2SO. These cyclic tetradepsipeptides do not contain N-substituted amino acid residues, and all the peptide and ester groups have been found to be transoid. Two conformers with very unequal populations have been found for AM-toxin I and II; the Cβ=Cα—C=O conformations of the Dha2 residues are nonplanar S-trans in the major conformer and nonplanar S-cis in the minor conformer. Only one ring conformation has been found for each of (L-Ala2) and (D-Ala2)AM-toxin I. (L-Ala2)AM-toxin I takes a C4-type ring conformation; all the C=O groups and Cα-H bonds are oriented to the same side of the ring. (D-Ala2)AM-toxin I takes a new ring conformation; the side chain and C=O group of the L-Amp1 residue are oriented to the same side of the ring. This new conformation is also found for the major conformers of AM-toxin I and II and thus appears to be required for the toxicity. The ring conformations of Tyr(OCH3)1-bearing analog tetradepsipeptides have been found to be much the same as those of Amp1-bearing depsipeptides. Furthermore, on the basis of the two distinct conformations of (D-Ala2) and (L-Ala2)AM-toxin I, an empirical rule is proposed for the stable ring conformations of cyclic tetra-D,L-peptides, not containing N-substituted amino acid residues.
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    Temperature-jump kinetics of the dC-G-T-G-A-A-T-T-C-G-C-G double helix containing a G·T base pair and the dC-G-C-A-G-A-A-T-T-C-G-C-G double helix containing an extra adenine (1983)
    New York : Wiley-Blackwell
    Biopolymers 22 (1983), S. 1235-1246 
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    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The kinetics of helix formation were investigated using the temperature-jump technique for the following two molecules: dC-G-T-G-A-A-T-T-C-G-C-G, which forms a double helix containing a G·T base pair(the G·T 12-mer), and dC-G-C-A-G-A-A-T-T-C-G-C-G, which forms a double helix containing an extra adenine (the 13-mer). When data were analyzed in an all-or-none model, the activation energy for the helix association process was 22 ± 4 kcal/mol for the G·T 12-mer and 16 ± 7 kcal/mol for the 13-mer. The activation energy for the helix-dissociation process was 68 ± 2 kcal/mol for the G·T 12-mer and 74 ± 3 kcal/mol for the 13-mer. Rate constants for recombination were near 105s-1M-1 in the temperature range from 32 to 47°C; for the dissociation process, the rate constants varied from 1s-1 near 32°C to 130s-1 near 47°C. Possible effects of hairpin loops and fraying ends on the above data are discussed.
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    Raman spectra and normal vibrations of dipeptides. II. Glycyl-L-proline (1983)
    New York : Wiley-Blackwell
    Biopolymers 22 (1983), S. 1285-1300 
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    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Raman and ir spectra of the glycyl-L-proline (GP) dipeptide were recorded. A normal-coordinate treatment was performed on the basis of the experimental spectra, using a modified Urey-Bradley force field (MUBFF). Cyclic redundancies were eliminated, and those due to the ring methylene groups, particularly distorted in regard to the tetrahedral conformation, were treated. An assignment of the experimental frequencies is proposed on the basis of the normal treatment.
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    Secondary structure of peptides. 4: 13C-Nmr CP/MAS investigation of solid oligo- and poly(L-alanines) (1983)
    New York : Wiley-Blackwell
    Biopolymers 22 (1983), S. 1357-1372 
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    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Primary and tertiary amine-initiated polymerizations of L-alanine-N-carboxyanhydride (L-Ala-NCA) were conducted at 20 or 100°C in a variety of solvents. The 75.5-MHz 13C-nmr CP/MAS spectra of the resulting poly(L-alanines) revealed that all samples contain both α-helix and pleated-sheet structures. Depending on the reaction conditions the α-helix content varied between ca. 1 and 99%. Reprecipitation from aprotic nonsolvents does not change the α-helix/β-sheet ratio, indicating that this ratio is thermodynamically controlled. Since relatively large amounts of oligopeptides of degree of polymerization (DP) 4-6 can be extracted by means of acetic acid, it is concluded that (a) most poly(L-alanines) possess a bimodal molecular weight distribution, (b) the oligopeptide fraction with DP ≤ 11 is responsible for the β-sheet fraction of all samples, and (c) the two-stage crystal growth proposed by Komoto and Kawai is not correct. Solubilizing initiators such as poly(ethylene oxide) NH2 prevent the precipitation of oligoalanine and, thus, the formation of a β-sheet structure. 13C-nmr CP/MAS measurements also show that tri- and tetra-L-alanines form insoluble β-sheet structures.
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    Interactions of molecules with nucleic acids. VII. Intercalation and T·A specificity of daunomycin in DNA (1984)
    New York : Wiley-Blackwell
    Biopolymers 23 (1984), S. 139-158 
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    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Intercalation complexes of daunomicin(+1) with tetramer duplexes in DNA are studied with the theoretically determined intercalation sites (I, -0.4), (II, -0.4), and (III, -1.4). These sites occur with base pairs separated by 6.76 Å for helical angles of 26°, 22°, and 8° about the intercalation site. Site I is preferred, and this is in agreement with experimental unwinding angles. Optimum binding positions and conformations are established, and these are in agreement with experimental results from crystal structures. A systematic procedure is devised to study base-pair and base-sequence specificity, which results in the demonstration that the most stable sequences are mainly ↑BP1, T·A, DAUN, A·T, BP4↓ and ↑BP1, T·A, DAUN, G·C, BP4↓, i.e., with the TpA and CpG (pyrimidine)p(purine) sequences about the intercalation site. These 32 possible sequences are found among the 40 most stable complexes. These theoretical calculations of intercalation complexes with daunomicin(+1) provide the first example in which a drug specifically selects the base pair T·A and prefers it in a particular sequence about the intercalation site. This specificity is in agreement with some experimental results. Problems associated with the interpretation of specificity are discussed in terms of the base, base-pair, and base-sequence resulting from the DNA site and the DNA-drug interactions. T·A specificity is rationalized by noting that the 2′deoxyribo-5′-monophosphate backbone attached to A is slightly more negative than that on the other nucleotides. Hence, a preference exists for binding to the protonated daunosamine (+1) groups. Stereographic projections of daunomycinone and daunomycin(+1) in a bond model and in a space-filling model with steric contours illustrate the results.
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    Small-angle x-ray scattering studies on yeast inorganic pyrophosphatase and its interactions with divalent metal ions, inorganic phosphate, and hydroxymethane bisphosphonate (1984)
    New York : Wiley-Blackwell
    Biopolymers 23 (1984), S. 159-165 
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    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Small-angle x-ray scattering studies have been carried out on the enzyme yeast inorganic pyrophosphatase (PPase), and its overall conformational changes on interaction with divalent metal ions (Mg2+ and Mn2+) and with phosphoryl ligands [inorganic phosphate (Pi) and hydroxymethane bisphosphonate (PCHOHP), a nonhydrolyzable inorganic pyrophosphate analog] were assessed. The enzyme undergoes an apparent reduction in size on simultaneous addition of Mg2+ and high Pi concentration, although neithough neither Mg2+ nor Pi added separately induced any measurable conformational changes. By contrast, simultaneous addition of Mn2+ and Pi to PPase does not result in an observable conformational change. However, the overall structure of the enzyme appears to enlarge in the simultaneous presence of Mn2+ ions and PCHOHP. The significance of the structural changes seen in PPase under various conditions is discussed.
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    Interacalation of ethidium ion into DNA and RNA oligonucleotides (1984)
    New York : Wiley-Blackwell
    Biopolymers 23 (1984), S. 213-233 
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    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The thermodynamics of ethidium ion binding to the double strands formed by the ribooligonucleotides rCA5G + rCU5G and the analogous deoxyribo-oligonucleotides dCA5G + dCT5G were determined by monitoring the absorbance versus temperature at 260 and 283 nm at several concentrations of oligonucleotides and ethidium bromide. A maximum of three ethidium ions bind to the oligonucleotides, which is consistent with intercalation and nearest-neighbor exclusion. For the ribo-oligonucleotide the binding mechanism is complex. Either two sites (assumed to be the intercalation sites at the two ends of the oligonucleotide) bind more strongly by a factor of 140 than the third site, or all sites are identical, but there is strong anticooperativity on binding (cooperativity parameter, 0.1). In sharp contrast, the binding to the same sequence (with thymine substituted for uracil) in the deoxyribo-oligonucleotide showed all sites equivalent and no cooperativity. For the ribo-oligonucleotides the enthalpy for ethidium binding is -14 kcal/mol. The equilibrium constants at 25°C depend on the model; either K = 6 × 105M-1 for the two strong sites (4 × 103M-1 for the weak site) or K = 2.5 × 105M-1 for the intrinsic constant of the anticooperative model. For the equivalent deoxyribo-oligonucleotide the enthalpy of binding is -9 kcal/mol and the equilibrium constant at 25°C is a factor of 10 smaller (K = 2.5 × 104M-1).
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    Distribution of counterions around a cylindrical polyelectrolyte and manning's condensation theory (1984)
    New York : Wiley-Blackwell
    Biopolymers 23 (1984), S. 287-312 
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    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The distribution of counterions around a charged polyion cylinder is calculated by several methods. First, the Debye-Hückel approximation is used, and it is shown that Manning's condensation hypothesis is necessry to avoid overneutralization of the polyion charges by the counterions when the linear-charge-density parameter, ξ, of the polyion exceeds the critical value of unity. However, it appears that this method of getting this result involves inconsistent application of Debye-Hückel theory. Therefore, we turn to the analytical solution of the Poisson-Boltzmann equation that was obtained by Alfrey, Berg, and Morawetz for a polyion cylinder plus a neutralizing number of counterions but without added salt. One of the integration constants of this solution is a radius, which we call RM, within which lies precisely the fraction of counterions that Manning assumes to condense in his theory. This radius can be rather large, however, so that the “Manning fraction” of condensed ions actually forms a diffuse cloud whose size varies with the polyelectrolyte concentration; RM varies as κ-1/2, where κ is the Debye-Hückel screening parameter. The Manning fraction, 1 - 1/ξ, and its associated radius are unique in their behavior with dilution; smaller fractions stay within finite radii, while with larger fractions the corresponding radii increase as κ-1. Thus, the condensation hypothesis does have a simple mathematical foundation in the Poisson-Boltzmann equation. Finally, by comparison with numerical solutions, we find that these conclusions are not significantly changed even when salt is added to the polyelectrolyte. A short table of numerical solutions of the Poisson-Boltzmann equation in cylindrical geometry is given, together with tables of coefficients tht enable one to discover the particular solution that applies for a given polyion radius and charge density.
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    Matrix-method calculation of linear and circular dichroism spectra of nucleic acids and polynucleotides (1984)
    New York : Wiley-Blackwell
    Biopolymers 23 (1984), S. 435-470 
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    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Calculations of the optical properties (absorption, linear dichroism, circular dichroism, and anisotropic components of the CD) are presented for polynucleotides of random or regular sequence within the formalism of the matrix method using a set of parameters that includes only the ππ* transitions of the aromatic bases. Experimental solution spectra agree favorably with calculated CD spectra for A-RNA, A-DNA, and B-DNA, when coordinates derived from x-ray studies on fibers are used. Excessive hypochromicity is predicted when parameters intended to reproduce the vacuum-uv absorption of the chromophores are included in the calculations, but total elimination of these parameters leads to an insufficient hypochromicity for the long-wavelength absorption band. Using alternative conformations for DNA in low-salt aqueous solution did not improve the agreement between experimental and calculated spectra, but some features of the optical properties predicted for these variant structures suggest that the tilt of the bases with respect to the helical axis may be larger than that of the fiber B-form.In the case of polynucleotides with regular structure, which have been traditionally less easy to understand in terms of the standard nucleic acid conformations, a series of alternative structures has been examined. Unexpectedly, the calculated spectrum for the Z-DNA structure compares almost quantitatively with the experimental spectrum of poly(dGC·dGC) in low salt. This result, which confirms a recent report [Vasmel, H. & Greve, J. (1981) Biopolymers 20, 1329-1332], is in contrast with the current identification of Z-DNA with the high-salt form of poly(dGC·dGC). Finally, the optical properties of single-stranded polyribonucleotides appear to be better explained when alternative structures [91-helix for poly(rA) and 61-helix for poly(rC)] are introduced instead of the A-RNA form.
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    Synthesis and conformation of the cyclic octapeptides cyclo(Phe-Pro)4, cyclo(Leu-Pro)4, and cyclo[Lys(Z)-Pro]4 (1983)
    New York : Wiley-Blackwell
    Biopolymers 22 (1983), S. 2191-2206 
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    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Cyclic octapeptides, cyclo(X-Pro)4, where X represents Phe, Leu, or Lys(Z), were synthesized and their conformations investigated. A C2-symmetric conformer containing two cis peptide bonds was found in all of these cyclic octapeptides. The numbers of available conformations due to the cis-trans isomerization of Pro peptide bonds depended on the nature of the solvent and X residue: they decreased in the following order: cyclo[Lys(Z)-Pro]4 〉 cyclo(Leu-Pro)4 〉 cyclo(Phe-Pro)4 in CDCl3. 13C spin-lattice relaxation times (T1) of these cyclic octapeptides were measured, and the contribution of segmental mobility to T1 was found to vary with the nature of the X residue.
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    Total intensity light scattering from short, optically anisotropic wormlike chains (1984)
    New York : Wiley-Blackwell
    Biopolymers 23 (1984), S. 607-608 
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    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
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    URL: http://dx.doi.org/10.1002/bip.360230314
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    Dimensions of short, rodlike macromolecules from translational and rotational diffusion coefficients. Study of the gramicidin dimer (1984)
    New York : Wiley-Blackwell
    Biopolymers 23 (1984), S. 611-615 
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    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Additional Material: 1 Ill.
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    URL: http://dx.doi.org/10.1002/bip.360230402
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    Alternative pathways in diffusion-collision controlled protein folding (1984)
    New York : Wiley-Blackwell
    Biopolymers 23 (1984), S. 675-694 
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    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The diffusion-collision model of protein folding has been solved exactly for a three-microdomain protein subunit. Numerical analysis shows that the exact kinetics may be excellently approximated in all cases studied by a standard chemical kinetics approach with the forward rate constants calculated from the mean folding time formula found previously.
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    Electric birefringence study of the purple membrane of Halobacterium halobium (1984)
    New York : Wiley-Blackwell
    Biopolymers 23 (1984), S. 707-718 
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    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: An electric birefringence study was carried out on aqueous suspensions of the purple membrane of Halobacterium halobium. In addition to the characterization of both native and modified membrane samples, the dependence of electric birefringence on pH and ionic strength was also investigated. The results indicate that purple membrane shows electric birefringence at a field strength as low as 200 V/cm. The permanent dipole moment and polarizability ranged from 20,500 debyes and 1.01 × 10-14 cm3 for a purple membrane concentration of 0.40 mg/mL to 41,000 debyes and 2.05 × 10-14 cm3 for a concentration of 0.80 mg/mL. It was also found that removal of the retinyl group of bacteriorhodopsin substantially decreases but does not eliminate the electric birefringence of the membrane. The solubilization of the membrane by Triton X-100, however, completely abolishes the electric birefringence. These experiments indicate that there is an interaction between adjacent bacteriorhodopsin molecules within the purple membrane via the retinyl chromophore moiety that builds up the permanent dipole moment. They also suggest that there are two types of response when purple membrane suspensions are placed in an electric field. One is an alignment of the disk-shaped particles with the field. The other is a stacking of the particles following their alignment by the electric field, which is promoted by the induced dipole moment.
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    Folded β-turns and collagenlike conformations of -Gly-Pro- and -Pro-Gly-sequences in synthetic polytripeptides (1984)
    New York : Wiley-Blackwell
    Biopolymers 23 (1984), S. 617-621 
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    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
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    Apparent molar volumes of some amino acids and peptides in aqueous urea solutions (1983)
    New York : Wiley-Blackwell
    Biopolymers 22 (1983), S. 2397-2409 
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    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Densities of solutions of several α-amino acids and peptides in 3 and 6m aqueous urea solvents have been determined at 298.15 K. These data have been used to evaluate the infinite-dilution apparent molar volumes of the solutes and the volume changes due to transfer (Vtr0) of the α-amino acids and peptides at infinite dilution from water to aqueous urea solutions. The sign and magnitude of the Vtr0 values have been rationalized in the framework of Friedman's cosphere-overlap model. The Vtr0 values for the glycyl group (—CH2CONH—) and alkyl side chains have been estimated.
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    Influence of conformation on the fluorescence of tryptophan-containing peptides (1983)
    New York : Wiley-Blackwell
    Biopolymers 22 (1983), S. 2459-2476 
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    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Conformational-energy calculations of the zwitterionic forms of Trp, Gly-Trp, Pro-Trp, Phe-Trp, Trp-Gly, Trp-Phe, Trp-Trp, and Trp-Gly-Gly were done using an empirical energy program for peptides (ECEPP). The resulting low-energy conformations were analyzed for the presence of hydrogen bonds, the distances between carbonyl groups and the indole ring, the distances between the N-terminal amino group and the indole ring, the dihedral angle between the planes containing carbonyl groups and the indole ring, and for dipeptides with two aromatic side chains, the dihedral angle and distance between the planes of the aromatic rings. This information was correlated with literature data from x-ray crystallographic studies, fluorescence lifetime studies, and quantum-yield experiments; proposed models of intramolecular quenching are discussed in light of the peptide conformations.
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    19F-NMR study of DNA bis-intercalation (1983)
    New York : Wiley-Blackwell
    Biopolymers 22 (1983), S. 2497-2500 
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    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
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    Geometry and mechanics of DNA superhelicity (1983)
    New York : Wiley-Blackwell
    Biopolymers 22 (1983), S. 2477-2495 
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    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: This paper analyzes the elastic equilibrium conformations of duplex DNA constrained by the constancy of its molecular linking number, Lk. The DNA is regarded as having the mechanical properties of a homogeneous, linearly elastic substance with symmetric cross section. Integral representations of the writhing number Wr and of Lk are developed, in terms of which the equilibria are given as solutions to an isoperimetric problem. It is shown that the Euler angles defining equilibrium conformations must obey equations identical to those governing unconstrained equilibria. A scaling law is developed stating that molecules supercoiled the same amount ΔLk will have geometrically similar elastic equilibria regardless of their length. Thus, comparisons among molecules of properties related to their large-scale tertiary structure should be referred to differences in ΔLk rather than to their superhelix densities. Specific conditions on the elastic equilibrium conformations are developed that are necessary for ring closure. The equilibrium superhelical conformations accessible to closed-ring molecules are shown to approximate toroidal helices. Questions relating to the stability and nonuniqueness of equilibria are treated briefly. A comparison is made between these toroidal conformations and interwound configurations, which are shown to be stable, although they are not equilibria in the present sense. It is suggested that entropic factors are responsible for favouring the toroidal conformation in solution.
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    Computer building of β-helical polypeptide models (1984)
    New York : Wiley-Blackwell
    Biopolymers 23 (1984), S. 23-38 
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    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: A general method is presented for computing the atomic coordinates of helices in which a dipeptide is the repeating unit. The method will generate both single- and double-stranded model helices having idealized bond lengths and angles, and any arbitrary, user-specified, pitch and number of residues per turn. The variation of inter- and intrastrand hydrogen bonds with pitch and number of residues per turn can thus be examined. An application of the method is the construction of a β-helix having pitch of 6.3 Å per turn and 4.85 residues per turn, a model which can pack nicely into the unit cell of crystals of cation-bound gramicidin A.
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    Conformational change in yeast tRNAAsp (1984)
    New York : Wiley-Blackwell
    Biopolymers 23 (1984), S. 71-81 
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    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The structure of yeast tRNAAsp in aqueous solutions has been analyzed in the light of results obtained from Raman spectra recorded at from 5 to 82°C and compared to those of tRNAPhe. Firm evidence is given of a reversible conformation transition for tRNAAsp at 20°C. This transition is observed for the first time in the tRNA series. The low-temperature conformation appears to have a more regular ribose-phosphate backbone and a more effective G base-stacking. This conformational change, which occurs essentially in the D loop, could be connected to the existence of two (A and B) crystal forms obtained depending on crystallization conditions. The melting temperatures, which are different for each base stacking in tRNAAsp, lie in a range of about 70°C, much higher than for tRNAPhe. This fact is interpreted by a higher ratio of G-C base pairs in tRNAAsp.
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    Interaction of poly-5-bromouridylic acid. I. Formation of helical complexes with various adenine and 2-aminoadenine derivatives (1984)
    New York : Wiley-Blackwell
    Biopolymers 23 (1984), S. 493-509 
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    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Complexes of poly(BU) with various adenine derivatives were investigated by circular dichroism (CD) and absorption spectroscopy. A 1:2 stoichiometry was indicated on CD mixing curves for typical complexes of 9-substituted adenine and 2-aminoadenine derivatives with poly(BU). The CD spectrum of adenosine·2poly(BU) is characterized by well-resolved bands in the range of 210-350 nm. Other adenine derivative-poly(BU) complexes also afford similar CD spectra, while 2-aminoadenine derivative-poly(BU) complexes give quite different spectra. Attempts to assign representative CD spectra were made using the transition of helical poly(BU) and the respective purine polynucleotides. The similarity of the CD spectra suggests that poly(A)·2poly(BU) and adenine derivative-poly(BU) complexes are nearly identical in structure except for the ribose-phosphate linkage. The fact that the uv isosbestic point of adenosine·2poly(BU) falls in close proximity to that of the corresponding polymer complex also supports this conclusion. In the formation of stable helices, the ribose moiety is dispensable in the “strand” of purine. The Tm of 9-methyladenine·2poly(BU) is somewhat higher than that of adenosine·2poly(BU) under equivalent conditions. The Tm difference with the monomer-poly(U) system was found to be about 20°C in 0.4M NaCl-0.02M Na-cacodylate-5 × 10-4M EDTA (pH 7.0). Further, it was noted that the monomer-poly(BU) complexes are formed even when the Tm is lower than that of self-folded poly(BU).
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    31P-NMR studies of deoxyoligonucleotides (1984)
    New York : Wiley-Blackwell
    Biopolymers 23 (1984), S. 575-592 
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    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The assignments of 31P resonances of eight short oligonucleotides have been achieved through specific heterodecoupling techniques reported previously from our laboratory [Cheng et al. (1982) Biopolymers 21, 697-701]. The temperature dependence of the assigned 31P chemical shifts of these oligomers was studied and compared to the constitutive dimeric units. This comparison gives some insight to the chemical-shift values of the phosphorus resonances of oligonucleotides. (1) The 3′-end terminal phosphorus resonance in an oligomer tends to locate at a spectral position relatively close to its constitutive dimeric unit. (2) On chain elongation (from 5′-toward 3′-end), the phosphorus resonance in the oligomer will be shifted upfield by 0.2-0.3 ppm, as compared to its constitutive dimeric unit. (3) The relative positions of phosphorus resonances in an oligomer tend to remain in the same order as their constitutive dimeric units. The above obsrvations lead to the development of a new procedure to assign the 31P resonance of a single-stranded oligonucleotide.
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    L-Alanyl-glycylglycine: FT-IR and Raman spectroscopic evidence for tripeptide packing in a collagenlike arrangement (1984)
    New York : Wiley-Blackwell
    Biopolymers 23 (1984), S. 623-627 
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    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Additional Material: 2 Ill.
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    Viscometry and sedimentation equilibrium of partially hydrolyzed hyaluronate: Comparison with theoretical models of wormlike chains (1984)
    New York : Wiley-Blackwell
    Biopolymers 23 (1984), S. 647-666 
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    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Fractionated samples of sodium hyaluronate of low molecular weight were used to calibrate the carbazole method for glucuronyl analsis and to determine the density increment (based on dry weight) of 0.444 (±0.003) mL/g in water and 0.386 (±0.003) mL/g for samples dialyzed against 0.2M NaCl. Weight-average molecular weights obtained by high-speed sedimentation equilibrium were used to calibrate the limiting viscosity number [η] in 0.2M NaCl, which gave [η]/Mw = 0.0028 (±0.0002) mL/g, valid to Mw = 0.0028 (±0.0002) mL/g, valid to Mw = 105. Experimental data from this work and the literature, including viscosity and light- and small-angle x-ray scattering measurements, were compared to theoretical chain models of the Kratky-Porod (KP) wormlike and the helical wormlike (HW) chain, as treated by Yamakawa and collaborators. Although either model could be fitted to experimental data about equally well with consistent parameters, provided those for the HW chain were of weakly helical nature, calculation of the unperturbed meansquare end-to-end distance as a function of chain length from a conformational model favored the KP chain alternative. The parameters that provide the best fit to experimental data for the KP wormlike model are a persistence length of 4.5-5 nm and a diameter of 1.1 nm. The latter is resonable for a hydrated hydrodynamic cylinder in view of the approximate unhydrated value of 0.7 nm estimated from the density increment.
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    Cation-induced conformational changes in tRNA molecules (1984)
    New York : Wiley-Blackwell
    Biopolymers 23 (1984), S. 759-766 
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    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The uv absorption spectra and melting profiles of an initially ion-free solution of E. coli unfractionated tRNA are significantly modified by the addition of either Na+, Mg2+, or Mn2+ or of other first-series transition-metal ions such as Ni2+, Co2+, and Zn2+. The main effect of the addition of all monovalent or divalent cations examined is an increase of the ordered and stacking stabilized tRNA structure, as revealed by a drop in the absorption near 260 nm, as well as in the 4-TU absorption region. Sharp differences have, however, been detected in the 290-305-nm range in the presence of the various ions studied. When transition-metal ions were added to a tRNA solution, an absorption peak appeared at 294 nm. This effect is interpreted as a perturbation of the electronic structure of the bases due to direct binding of metal ions to the bases. An analysis of the variation in the spectrum as a function of metal concentration and of the thermal melting reversibility in the presence of various metal ions supports the conclusion that while all ions investigated are involved in binding to the phosphate groups of tRNA, transition-metal ions are also able to bind directly to the bases.
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    Electrostatic interactions between α-helix dipoles in crystals of an uncharged helical undecapeptide (1984)
    New York : Wiley-Blackwell
    Biopolymers 23 (1984), S. 809-817 
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    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The electrostatic interactions between α-helix dipoles in the crystals of an uncharged helical undecapeptide have been studied in detail. The electrostatic interaction energy between one helix dipole and its 26 nearest neighbors is approximately -23 kcal mol-1. A very similar result is obtained when calculating the interactions between one helix dipole and all 988 helix dipoles occurring within a distance of 75 Å. It therefore appears that in these crystals of completely uncharged molecules large, favorable electrostatic interactions occur.
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    Modeling biological macromolecules in solution. II. The general tri-axial ellipsoid (1984)
    New York : Wiley-Blackwell
    Biopolymers 23 (1984), S. 843-843 
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    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
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    URL: http://dx.doi.org/10.1002/bip.360230421
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    Most-probable distribution at enzyme depolymerization of polysaccharides (1984)
    New York : Wiley-Blackwell
    Biopolymers 23 (1984), S. 859-876 
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    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Several research groups have studied depolymerizing processes by enzyme cleavage using product distribution. Although only the shortest chain products can be measured experimentally, interpretation of much evidence requires an assumption of the nature of high polymer distribution. The present work analyzes the high polymer distribution of products on the basis of mathematical models suggested for the two most widespread α-amylase action-mechanisms. The most-probable distribution was found to be distorted by hydrolysis only for the shortest chain products. The size of the distorted region is directly dependent on the characteristics of a specific enzyme. We studied the distribution of products for substrates of varying composition to show that it approaches the most-probable distribution at depolymerization.
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    Conformation and folding in histones H1 and H5 (1983)
    New York : Wiley-Blackwell
    Biopolymers 22 (1983), S. 113-118 
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    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Denatured histones H1 and H5 can be readily refolded on salt addition. Their digestion by trypsin leads to limit peptides of about 80 residues having the same nmr and CD spectra as those of the intact parent histones. Scanning microcalorimetry shows that (1) the folded structures of H1 and H5 are located entirely in their limit peptides; (2) both have values of the specific denaturation enthalpy typical for small globular proteins; and that (3) both exhibit a classic “2-state” transition (ΔHdcal = ΔHdvan't Hoff). The heat-denaturation profiles of H5 measured using intrinsic and extrinsic Cotton effect and side-chain nmr peaks do not coincide at all. Only the intrinsic Cotton effects give a Tm and ΔHdvan't Hoff close to that from microcalorimetry. We conclude that these proteins exhibit large-scale side-chain motions that precede the macroscopic cooperative transition.
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    Cis-trans peptide-bond equilibria in cyclic hexapeptides (1983)
    New York : Wiley-Blackwell
    Biopolymers 22 (1983), S. 153-156 
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    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Data are presented on the position of the equilibria of cyclo(Xxx-Pro-Yyy)2 backbones between forms with two cis Xxx-Pro peptide bonds and forms with only trans peptide bonds. These data are interpreted in terms of two factors: a solvent-independent steric interaction between the Xxx and Pro side chains, and the ability of solvent to influence the transannular electrostatic interaction between N—H and C=O groups of the Xxx units in the all-trans form.
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    Influence of the peptide chain length on the stability of double-stranded β-helical species of D,L-alternating oligovalines in chloroform solution (1983)
    New York : Wiley-Blackwell
    Biopolymers 22 (1983), S. 157-161 
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    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The type and distribution of the β-helixes occurring in chloroform solutions of Boc-(L-Val-D-Val)6-OMe and Boc-(L-Val-D-Val)8-OMe have been studied by using 1H-nmr techniques. Right- and left-handed ↑↓β4.4-helices and left-handed β5.6-helices occur with the dodecapeptide. β4.4-Helices of opposite handedness occur also with the hexadecapeptide, but ↑↓β5.6-helices could not be detected with this oligomer. At equilibrium, at 25°C, the double helix of the dodecapeptide is only moderately populated. These results indicate that increasing the chain length has a destabilizing effect on the ↑↓β5.6-helices of D,L-alternating oligovalines in chloroform solution.
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    Preferred conformations of peptides containing α,α-disubstituted α-amino acidsThis is part 97 of the “linear oligopeptide series.” For part 96, see Bonora, G. M., Moretto, V., Toniolo, C. & Mutter, M. (1982) submitted to Int. J. Pept. Protein Res. (1983)
    New York : Wiley-Blackwell
    Biopolymers 22 (1983), S. 205-215 
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    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The conformational preferences of linear peptides containing α,α-disubstituted α-amino acids, derived from the crystal structures of 28 compounds, are reviewed. In particular, the sensitivity of peptide conformation to the geometry of these unusual amino acids is underlined. We also consider possible future directions of research, which, we hope, will result in a complete understanding of the structures adopted by peptaibol antibiotics.
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    Stabilizing effects of 2-methylalanine residues on β-turns and α-helices (1983)
    New York : Wiley-Blackwell
    Biopolymers 22 (1983), S. 241-246 
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    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: 13C-, 1H-nmr, CD, and x-ray crystallography revealed β-turns of type III for Boc-Gly-L-Ala-Aib-OMe, Boc-L-Ala-Aib-L-Ala-OMe; the 310-helix for Boc-Aib-L-Ala-Aib-L-Ala-Aib-OMe; and antiparallel arranged α-helices for Boc-L-Ala-Aib-Ala-Aib-Ala-Glu(OBzl)-Ala-Aib-Ala-Aib-Ala-OMe. An N-terminal rigid α-helical segment is found in the polypeptide antibiotics alamethicin, suzukacillin, and trichotoxin. The α-helix dipole is essential for their voltage-dependent pore formation in lipid bilayer membranes, which is explained by a flip-flop gating mechanism based on dipole-dipole interactions of parallel and antiparallel arranged α-helices within oligomeric structures.
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    Insulin's structural behavior and its relation to activity (1983)
    New York : Wiley-Blackwell
    Biopolymers 22 (1983), S. 281-291 
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    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: This paper discusses the hypothesis that insulin undergoes a conformational change either before or during its binding to the receptor. The evidence for this is not conclusive but allows us to reconcile the following observations: (1) no chemical modification or deletion of invariant surface residues has abolished the hormone's activity - only reduced its potency. (2) Reduction in potency follows many modifications to different side chains, both variant and invariant. (3) There are insulins with perfectly preserved structure (by the criteria of aggregation, spectroscopy, and x-ray analysis) that have markedly reduced potency. (4) Insulins with disturbed structure still exhibit real, sometimes substantial activity.
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    Refinement of the structure of bovine seminal ribonuclease (1983)
    New York : Wiley-Blackwell
    Biopolymers 22 (1983), S. 327-332 
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    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: We report here the refinement at 2.5-Å resolution of the x-ray crystal structure of bovine seminal ribonuclease, a dimeric covalent enzyme. The protein, which crystallizes with one molecule in the asymmetric unit, consists of two subunits of identical chemical sequences, related by an almost exact binary axis. The tertiary structure of the subunits is similar to that of the pancreatic enzyme, which shows similar catalytic properties. The refinement was carried out using the restrained least-squares procedure both in the reciprocal and real spaces. The assemblage of the subunits in the dimer is described and discussed.
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    Lateral and rotational diffusion of EGF-receptor complex: Relationship to receptor-mediated endocytosis (1983)
    New York : Wiley-Blackwell
    Biopolymers 22 (1983), S. 347-353 
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    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The clustering and internalization of epidermal growth factor (EGF)-receptor complexes on human tumor cells are temperature-sensitive processes that are completely inhibited at 4°C. The rotational diffusion of EGF-receptor is limited by the viscosity of the lipid matrix, while additional constraints limit the lateral diffusion of the receptor molecule. Although the lateral and rotational diffusion of the occupied receptors are temperature sensitive, they do not provide a rate-determining factor for the clustering and subsequent internalization of the EGF-receptor. Even at 4°C the occupied receptors move quickly enough to allow the formation of EGF-receptor clusters. The lack of internalization at 4°C must be due to the inhibition of interactions other than a temperature effect on receptor mobility. EGF-induced receptor clustering involves the formation of microclusters composed of 10-50 receptor molecules.
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    Photo-CIDNP study of interactions of serine proteinases with their protein inhibitors (1983)
    New York : Wiley-Blackwell
    Biopolymers 22 (1983), S. 387-390 
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    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Photochemically induced dynamic nuclear polarization was used to study the accessibility of surface tyrosine and tryptophan residues in proteinases, in their protein inhibitors and in the proteinase-inhibitor complexes. The accessibility probe is the triplet of 10-(carboxyethyl) flavin formed by optical excitation. On complex formation we observe accessibility loss in the surface tyrosines and tryptophans in the proximity of the proteinase-inhibitor contact site, and in the case of bovine pancreatic trypsin inhibitor, in more distant tyrosines as well.
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    Peptides as channel-making ionophores: Conformational aspects (1983)
    New York : Wiley-Blackwell
    Biopolymers 22 (1983), S. 403-407 
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    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The β62.4- and β126.6-helical structures do not appear consistent with the structural data and ion-transport properties of (Ala-Ala-Gly) or (Leu-Ser-Leu-Gly) oligomers. Oligoalanine derivatives also give rise to current fluctuations in bilayer lipid membranes. Bundles of molecules may explain the behavior of these various peptides in membranes.
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    Contribution of synthetic polymers of amino acids to knowledge of immune response (1983)
    New York : Wiley-Blackwell
    Biopolymers 22 (1983), S. 441-452 
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    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The synthetic random polymers poly(Glu,Lys,Phe), poly(Glu,Phe) and poly(Glu,Lys,Tyr), have been used to study some parameters associated with the genetic control of the immune response (Ir) of mice. Mice of haplotypes d and q respond well to GLPhe. Mice of haplotypes k and b were previously shown to be nonresponders, whereas the F1 (k × b) responded via a phenomenon involving “complementation” between 2 Ir genes, i.e., one gene product from IA, and another from IE form the requisite two-chain Ia “receptor” macromolecules (EbβEkα). When it was determined that mice of haplotypes q and k respond to GPhe, and the controlling gene maps to IA, (Aα Aβ), we tested the theory that mice having q and k alleles in IA might respond to GLPhe via recognition of GPhe determinants in the terpolymer. Employing the in vitro proliferative response to T-cells from mice immunized with GLPhe and stimulated with GPhe and GLT (cross-reaction), it was determined that different determinant selection patterns exist in the recognition of GLPhe. Mice having q and k alleles in IA can respond to GLPhe via one mechanism, and other mice having d and f alleles respond via other mechanisms. The F1 of the appropriate nonresponder strains forming the Ia molecule (EbβEkα) still exhibit the “complementation” phenomenon. Rabbit antibody against anti-GPhe (ID) from SWR mice (H-2q)(anti-ID) was prepared. This anti-ID strongly inhibited the binding of 125I-GPhe by anti-GPhe antisera produced only in mice of H-2q haplotype and had no effect on the binding of GPhe by anti-GPhe antisera produced in mice of other haplotypes. The anti-ID also inhibited the binding of 125I-GLPhe and 125I-GPhe by anti-GLPhe antisera produced only in mice of H-2q haplotype. These specificities were also confirmed by the inhibition of the plaque-forming cells. It was concluded that the antibodies produced in mice of H-2q haplotype against GPhe and GLPhe share common idiotypic determinants that are recognized by the anti-idiotypic antiserum.
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    Immunoassays of peptide hormones and their chemical aspects (1983)
    New York : Wiley-Blackwell
    Biopolymers 22 (1983), S. 481-486 
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    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The N-terminal maleoyl-β-alanyl derivative of human gastrin-[2-17] has been synthesized as a model compound to investigate the usefulness of such peptide derivatives for their mild and selective conjugation, via reaction with thiol groups, to high-molecular-weight carrier molecules to produce antigens, as well as to radioiodinable or fluorogenic molecules to prepare tracers for immunoassays. In this context the examined enzyme substrate-gastrin conjugate was found to exhibit the full immunoreactivity of the parent peptide and to be well suited as tracer in a gastrin fluorescence-immunoassay.
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    Field desorption mass spectra of dermorphin and some related peptides (1983)
    New York : Wiley-Blackwell
    Biopolymers 22 (1983), S. 487-491 
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    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Additional Material: 2 Ill.
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    Controlled release of macromolecules and pharmaceuticals from synthetic polypeptides based on glutamic acid (1983)
    New York : Wiley-Blackwell
    Biopolymers 22 (1983), S. 547-556 
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    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Biocompatible, biodegradable copolymers of glutamic acid and ethyl glutamate were evaluated for their permeability to proteins ranging in molecular weight from 12,300 to 69,000. The results showed that the copolymers were sufficiently permeable that they could be used for the preparation of implantable, controlled-release systems capable of releasing therapeutic amounts of high-molecular-weight drugs.
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    Temperature dependence of the diffusion coefficient of polystyrene latex spheres (1983)
    New York : Wiley-Blackwell
    Biopolymers 22 (1983), S. 593-595 
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    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Additional Material: 1 Ill.
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    Conformational study of ribonucleotides, 2′-deoxyribonucleotides, and arabinonucleotides by carbon-13 nuclear magnetic resonance (1983)
    New York : Wiley-Blackwell
    Biopolymers 22 (1983), S. 605-616 
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    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The geminal and vicinal 13C-31P coupling constants have been monitored, as a function of pH, for a series of uracil and cytosine 3′- and 5′-nucleotides with a ribose, arabinose, or 2′-deoxyribose sugar. Data were also obtained for two 3′,5′-diphosphates in the ribose and arabinose series. The geminal J(C5′-P5′) and J(C3′-P3′) couplings show only a small dependence on the ionization state of the phosphate, decreasing by 〈 0.5 Hz in the pH 5-7 range. For the ribose and arabinose 3′-nucleotides, the vicinal J(C4′-P3′) increase (up to 1.5 Hz) on secondary phosphate ionization in the pH 5-7 range, whereas their J(C2′-P3′) couplings decrease (up to 1.5 Hz) over the same pH range. In contrast for the 2′-deoxyribose molecules, both couplings decrease (∼0.5 Hz) on phosphate ionization. The titration curves provide information about the influence of the sugar on the conformation about the C3′—O3′ bond. Some conformational trends could be rationalized by consideration of the sugar-puckerdependent contact interactions between the 3′-phosphate and the substituents on the furanose ring.
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    Copolymerization kinetics of N-carboxyanhydrides of some α-amino acids: Influence of nature of amino acids (1983)
    New York : Wiley-Blackwell
    Biopolymers 22 (1983), S. 747-753 
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    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Studies on copolymerization kinetics of N-carboxyanhydride (NCA) of O-acetyl-L-tyrosine (T) with NCAs of L-valine (V) and glycine (G) were carried out in dioxane at 25°C with n-butylamine as initiator. The reactivity ratios for the VT system were found to be rV:rT:0.57:0.22; and for the GT system, rG:rT:0.26:0.42. A comparison of this data with that obtained when L-analine was used in place of L-valine or glycine showed that in the three systems, the reactivity ratio of the amino acid residue with a greater tendency to form ordered secondary structure was greater than that of its comonomer. Among the variable comonomers (glycine, L-alanine, L-valine) of O-acetyl-L-tyrosine, it is again L-alanine, whose tendency to form helical structure is very high, that has the greater reactivity ratio.
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    Conformation of the central sequence of angiotensin II and analogs (1983)
    New York : Wiley-Blackwell
    Biopolymers 22 (1983), S. 663-687 
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    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: We describe the synthesis and the conformational analysis by ir, CD, and proton-nmr spectroscopy of four model peptides of the type N-Ac-Tyr-X-His-NH2 with X = Val, Leu, Ala, Gly. These peptides represent the central sequence of the hormone angiotensin II and its position-5 analogs. We studied their conformational behavior in aqueous solution during pH titration and in organic solvents. For specific purposes of spectral analysis (ir band assignment, proton-nmr signal assignment, heteronuclear vicinal coupling constants), we synthesized three isotopically enriched homologs of the mother sequence, i.e., N-Ac-(15N-Tyr)-Val-His-NH2, N-Ac-(13C, 2H, Tyr)-Val-His-NH2, and N-Ac-Tyr-(13C, 2H, Val)-His-NH2. Results are summarized as follows: the tyrosine and the histidine side chains influence each other through space; this mutual influence is modulated by the nature of the side chain in position X and decreases in going from X=Val to X=Gly as a consequence of two simultaneous events, changes in the side-chain rotamer distribution and changes in the ϕ and ψ angles of residue X. The decrease in the bulkiness of the side-chain X (Val → Gly) leads to increased flexibility of the peptide backbone at this site, which is also reflected in the apparent ratio of C5, C7, and intermediate conformations present in equilibrium. The three spectroscopic techniques, in addition to the results of chymotryptic degradation experiments, show a high level of agreement, and all reflect the dynamic conformation of these peptides in a different manner.
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    Assignment of the amide and aromatic protons of the CHA2-dodecapeptide α-factor from S. Cerevisiae (1983)
    New York : Wiley-Blackwell
    Biopolymers 22 (1983), S. 815-820 
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    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Additional Material: 2 Ill.
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    Conformation study on heparin by intermediate-angle X-ray scattering (1984)
    New York : Wiley-Blackwell
    Biopolymers 23 (1984), S. 995-1009 
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    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The conformation of heparin in water was investigated by intermediate-angle x-ray scattering (IAXS). The theoretical scattering function for the coil conformation was calculated by the Monte Carlo method using the approximation of separable conformation energies and the conformation energies computed for two disaccharide pairs in heparin. From x-ray scattering in a relatively small-angle region, the conformation of heparin is not the ordered 21 helix conformation but the coil conformation obtained by the Monte Carlo calculation. It is expected, from x-ray scattering in a relatively wide-angel region, that the sulfate groups of heparin maintain about 7 Å between them.
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    Study of polysaccharides by the fluorescence method. III. Chain length dependence of the micro-Brownian motion of amylose in an aqueous solution (1984)
    New York : Wiley-Blackwell
    Biopolymers 23 (1984), S. 1043-1056 
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    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The fluorescence polarization method was applied to the investigation of the micro-Brownian motion of amylose chains having a wide range of degree of polymerization (DP). We prepared two types of fluorescent conjugates of amylose: amylose conjugated with fluorescein randomly throughout the chain (F-amylose) and amylose conjugated locally on a terminal segment (t-F-amylose). The degree of fluorescence polarization of these conjugates was measured by changing the solvent viscosity at a constant temperature (25°C). The data obtained were analyzed by a Perrin-type equation to calculate the mean rotational relaxation time, 〈ρ〉. By examination of the plots of 〈ρ〉 vs DP, and by comparison of 〈ρ〉 with the theoretical rotational relaxation time of the whole molecule at a given DP, it was found that 〈ρ〉 mainly reflects the segmental motion of the amylose chain in the high-DP range. Thus, the fact that 〈ρ〉 for t-F-amylose is much smaller than that for F-amylose at a sufficiently high DP shows that a terminal segment undergoes a more rapid micro-Brownian motion than interior segments. In the low-DP range, we felt that the rotational diffusion of the whole molecule contributes significantly to the relaxation process. We also examined, for comparison, the segmental motion of dextran and pullulan in a similar manner and found that these segmental motions are more rapid than those of amylose. Based on the results obtained, the segmental mobility and conformation of the amylose molecule are discussed in relation to its chain length.
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    Synthesis and properties of L-cysteinyl-L-cysteine disulfides (1984)
    New York : Wiley-Blackwell
    Biopolymers 23 (1984), S. 1085-1097 
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    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Oligomeric cyclic disulfides, obtained by mild oxidation of the fully protected dipeptide L-cysteinyl-L-cysteine, have been isolated by gel and thin-layer chromatography. Polymeric material was recycled by a thiol-disulfide exchange-reaction performed at basic pH. Spectroscopic investigations of the monomer and the two dimers indicate that conformers characterized by dihedral angles about the S—S bond close to ±90° are preferred. Moreover, chiroptical and 1H-nmr data for these compounds suggest higher mobility for the two dimers. The antiparallel dimeric disulfide can be considered a model compound for the hinge region formed at the subunit interface of the bovine seminal ribonuclease, a dimeric enzyme showing a complex kinetic behavior.
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    Dynamic light scattering as a probe of superhelical DNA-intercalating agent interaction (1984)
    New York : Wiley-Blackwell
    Biopolymers 23 (1984), S. 1113-1119 
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    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Polarized dynamic light-scattering measurements on superhelical pBR322-plasmid DNA solutions in 0.2M NaCl, 2 mM NaPi, pH 7.0, 2 mM EDTA result in a translational diffusion coefficient DT,20°C0 = (3.77 ± 0.10) × 10-8 cm2/s for the native molecule. Modeling the DNA, in the simplest approximation, as a 10 × 440-nm effective hydrodynamic rigid rod yields a good fit to the apparent diffusion coefficient angular-dependence data up to 70°; the model fails at higher angles, probably due to the effects of flexibility or branching of the rod. Diffusion coefficient titration experiments with a platinum complex intercalating agent (PtTS) result in a titratable superhelix density of σ = -0.079 ± 0.008 under our experimental conditions, corresponding to about 34 superhelical turns in the native DNA. The DNA contour length predicted by our two independent results, the rod dimensions and the number of superhelical turns, is in excellent agreement with the contour length calculated from the number of base pairs, supporting the hydrodynamic approximation of an effective rodlike structure for this small DNA molecule in solution.
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    Quasi-harmonic method for studying very low frequency modes in proteins (1984)
    New York : Wiley-Blackwell
    Biopolymers 23 (1984), S. 1099-1112 
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    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: A quasi-harmonic approximation is described for studying very low frequency vibrations and flexible paths in proteins. The force constants of the empirical potential function are quadratic approximations to the potentials of mean force; they are evaluated from a molecular dynamics simulation of a protein based on a detailed anharmonic potential. The method is used to identify very low frequency (∼1 cm-1) normal modes for the protein pancreatic trypsin inhibitor. A simplified model for the protein is used, for which each residue is represented by a single interaction center. The quasi-harmonic force constants of the virtual internal coordinates are evaluated and the normal-mode frequencies and eigenvectors are obtained. Conformations corresponding to distortions along selected low-frequency modes are analyzed.
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    Temperature dependence of the dynamic light scattering of linear φ29 DNA: Implications for spontaneous opening of the double-helix (1984)
    New York : Wiley-Blackwell
    Biopolymers 23 (1984), S. 1137-1137 
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    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
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    URL: http://dx.doi.org/10.1002/bip.360230613
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    Contributions of synthetic polymers of amino acids to knowledge of immune response (1984)
    New York : Wiley-Blackwell
    Biopolymers 23 (1984), S. 1141-1141 
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    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
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    URL: http://dx.doi.org/10.1002/bip.360230615
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    Interaction of poly(I)·poly(C) with trans-dichloro-diammine-platinum (II) (1984)
    New York : Wiley-Blackwell
    Biopolymers 23 (1984), S. 1143-1143 
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    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
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    URL: http://dx.doi.org/10.1002/bip.360230616
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    Analysis of the high- and low-spin soret bands of horse-heart metmyoglobin complexes (1984)
    New York : Wiley-Blackwell
    Biopolymers 23 (1984), S. 1147-1167 
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    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Interest in the thermodynamics of the iron-binding site in hemoproteins has increased in recent years due to refinements in x-ray crystallographic studies of hemoproteins [see Deathage, J. F., Lee, R. S., Anderson, C. M. & Moffat, K. (1976) J. Mol. Biol. 104, 687-706; Heidner, E. J., Ladner, R. C. & Perutz, M. F. (1976) J. Mol. Biol. 104, 707-722; Deathage, J. F., Lee, R. S. & Moffat, K. (1976) J. Mol. Biol. 104, 723-728; Ladner, R. C., Heidner, E. J. & Perutz, M. F. (1976) J. Mol. Biol. 114, 385-414; Fermi, G. & Perutz, M. F. (1977) J. Mol. Biol. 114, 421-431; Takano, T. (1977) J. Mol. Biol. 110, 537-568 and 569-589], the synthesis and x-ray analysis of model heme compounds [see Scheidt, W. R. (1977) Acc. Chem. Res. 10, 339-345; Kastner, M. E., Scheidt, W. R., Mashino, T. & Reed, C. A. (1978) J. Am. Chem. Soc. 100, 666-667; Mashiko, T., Kastner, M. E., Spartalian, K., Scheidt, W. R. & Reed, C. A. (1978) J. Am. Chem. Soc. 100, 6354-6362; Hill, H. A. O., Skite, P. P., Buchler, J. W., Luchr, H., Tonn, M., Gregson, A. K. & Pellizer, G. (1979) Chem. Commun. 4, 151-152; and Scheidt, W. R., Cohen, I. A. & Kastner, M. E. (1979) Biochemistry 18, 3546-3556], and the numerous data on heme-protein interactions that account for the differences observed in ligand binding between the various species of animals. Numerous probes have been used and provide information about the structure and thermodynamics of the binding site, but no single probe can provide the complete picture [see Iizuka, T. & Yonetani, T. (1970) Adv. Biophys. 1, 157-182; Smith, D. W. & Williams, R. J. P. (1970) Struct. Bond. 7, 1-45; and Spiro, T. G. (1975) Biochim. Biophys. Acta 416, 169-189].
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    Conversion from a virtual-bond chain to a complete polypeptide backbone chain (1984)
    New York : Wiley-Blackwell
    Biopolymers 23 (1984), S. 1207-1224 
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    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: A method for generating a complete polypeptide backbone structure from a set of Cα coordinates is presented. Initial trial values of φ and ψ for a selected residue are chosen (essentially from an identification of the conformational region of the virtual-bond backbone, e.g., and α-helical region), and values of φ and ψ for the remaining residues (both towards the N- and C-terminus) are then computed, subject to the constraint that the chain have the same virtual-bond angles and virtual-bond dihedral angles as the given set of Cα coordinates. The conversion from Cα coordinates to full backbone dihedral angles (φ,ψ) involves the solution of a set of algebraic equations relating the virtual-bond angles and virtual-bond dihedral angles to standard peptide geometry and backbone dihedral angles. The procedure has been tested successfully on Cα coordinates taken from standard-geometry full-atom structures of bovine pancreatic trypsin inhibitor (BPTI). Some difficulty was encountered with error-sensitive residues, but on the whole the backbone generation was successful. Application of the method to Cα coordinates for BPTI derived from simplified model calculations (involving nonstandard geometry) showed that such coordinates may be inconsistent with the requirement that φPro be near -75°. In such a case, i.e., for residues for which the algebraic method failed, a leastsquares minimizer was then used in conjunction with the algebraic method; the mean-square deviation of the calculated Cα coordinates from the given ones was minimized by varying the backbone dihedral angles. Thus, these inconsistencies were circumvented and a full backbone structure whose Cα coordinates had an rms deviation of 0.26 Å from the given set of Cα coordinates was obtained.
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    Conformation of P-form DNA (1984)
    New York : Wiley-Blackwell
    Biopolymers 23 (1984), S. 1269-1281 
    Details
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The P-Form of DNA has been studied by use of ir spectroscopy and electron microscopy (EM). The ir data show that the P-form has little or no hydrogen bonding, while the data from EM show that the P-form has a condensed tertiary structure. In earlier work, we demonstrated that the P-form is devoid of base stacking. When that information is combined with the new ir data, we conclude that the P-Form is denatured because it lacks any of the interactions associated with a normal secondary structure. This is in apparent contradiction to earlier work that showed that the P-form may be easily transformed back to a native state by adding water. However, the lack of secondary structure can be overcome by the presence of a collapsed tertiary state that does not allow non-hydrogen-bonded strands to separate. Thus, the complementary strands can renature quickly on addition of water. The collapse to a condensed tertiary structure occurs when roughly 90% of the charge on the DNA molecule is neutralized by counterion condensation, as calculated by the Manning polyelectrolyte theory, and is consistent with other collapsed DNA states in this respect. This structure explains all physical properties of the P-form that have been observed.
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    URL: http://dx.doi.org/10.1002/bip.360230711
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    The effects of alkali-metal chlorides and of spermidine and spermine on the swelling pressures of DNA gels in the ultracentrifuge (1984)
    New York : Wiley-Blackwell
    Biopolymers 23 (1984), S. 1307-1313 
    Details
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The effects is solution of the alkali-metal chlorides on the gel-like phase of DNA formed in the ultracentrifuge cell have been studied. The polycations, spermidine and spermine, also were shown to affect strongly the swelling pressure of the DNA gel, with evidence for the destabilization of DNA in very dilute spermine, below 10-6 M, and for the collapse of DNA in both spermine and spermidine solutions above 10-6 M.
    Additional Material: 3 Ill.
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    URL: http://dx.doi.org/10.1002/bip.360230714
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    Effect of cationic surfactants on the conformation and aggregation of poly(L-glutamic acid) (1984)
    New York : Wiley-Blackwell
    Biopolymers 23 (1984), S. 1333-1346 
    Details
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The effects of three cationic surfactants, dodecylammonium chloride (DAC), dodecyldimethylammonium chloride (DDAC), and dodecyldimethylammonium chloride (DTDAC), on the conformation of poly(L-glutamic acid) and at neutral pH were examined by CD. The maximum extent of the α-helix induction occurs for each surfactant when the mixing ration is about unity. Different effects specific to each surfactant, as described below, appear in the range of mixing ratios larger than that required for the maximum induction. In the case of DTAC, the α-helices disintegrate into random coils. In the case of DDAC, the aggregation of α-helices takes place eventually leading to precipitation. Solubilization of the precipitates occurs at high mixing ratios. The most complex behavior is seen in the case of DAC; aggregation of α-helices occurs only to a small extent and the formation of a small complex predominates over aggregation takes place again as DAC concentration increases further. Induction of the α-helix is favored by dilution at a constant mixing ratio but is suppressed by the addition of NaCl.
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    URL: http://dx.doi.org/10.1002/bip.360230717
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    Locally oscillatory motion of RNA helix derived from linear relationships of backbone torsion angles (1984)
    New York : Wiley-Blackwell
    Biopolymers 23 (1984), S. 1169-1184 
    Details
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: A linear relationship in each of the torsion angle pairs, α-β, β-∊, ∊-ζ, and α-γ, has been found by applying a statistical method based on the concept of circular variates to backbone torsion angle data of helical in yeast tTNAPhe. A series of helical dimer models generated with these relationships have been found to be stereochemically acceptable, and the models also indicate that the backbone unit in the RNA helix is geometrically capable of an oscillatory motion with the distance of about 3.4 Å between adjacent bases. The motion of the backbone unit is analogous to that of a helical spring. The adjacent bases, because of being attached to the backbone, oscillate in a manner similar to the oscillatory dimer model proposed by Davis and Tinoco [Davis, R. C. & Tinoco, I., Jr. (1968) Biopolymers 6, 223-242]. Here, the oscillation of the backbone unit in the RNA helix is discussed in terms of two geometrical quantities: the torsion (τ) and curvature (κ) of the helix. On these lines, a stereochemical model of RNA strand separation is proposed.
    Additional Material: 7 Ill.
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    URL: http://dx.doi.org/10.1002/bip.360230703
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    The speed of sound in DNA (1984)
    New York : Wiley-Blackwell
    Biopolymers 23 (1984), S. 1185-1192 
    Details
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: We have used Brillouin scattering to determine the speed of sound in (and hence longitudinal modulus of) A- and B-DNA fibers. The speed of sound is very sensitive to the degree of hydration of the fibers, and measurements have to be made at laser powers below 5 mW to avoid local heating and dehydration. Under those conditions, we obtain sound speed perpendicular to the fiber axis of about 2.2 and 1.9 km/s in A- and B-DNA fibers, respectively. A-DNA fibers show a small anisotropy with sound speeds along the fiber axis higher by up to 10% B-DNA fibers appear to be isotropic.
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    Interaction of metal ions with gastrointestinal hormones: Binding studies of Mg++ to biologically active analogs of little gastrin and minigastrin (1984)
    New York : Wiley-Blackwell
    Biopolymers 23 (1984), S. 1225-1240 
    Details
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The interaction of magnesium ions with Des-Trp1-Nle12-minigastrin I (Nle11-HG-13) and Nle115-little gastrin I (Nle15-HG-17) has been studied by CD and spectrophotometric techniques in trifluoroethanol. Spectrophotometric titrations using murexide as a metallochromic indicator showed that there are three binding sites for magnesium ions in Nle11-HG-13, with binding constants of the order of (6 ± 2) × 106, (1.7 ± 0.5) × 106, and (5.0 ± 0.5) × 105M-1. These figures have been independently confirmed by CD measurements in the far-uv in the presence of increasing amounts of magnesium ions. Elongation of the peptide chain from Nle11-HG-13 to Nle15-HG-17 does not provide any additional binding site for the metal ions. In both hormones, we have observed different responses in the near- and fur-uv CD properties with regard to added magnesium. The intensity of the CD bands in the aromatic region changes cooperatively with the ion/hormone molar ratio. These findings lead us to conclude that at the C-terminal, the biologically important sequence, -Trp-Nle-Asp-Phe-Nh2, is directly involved in the interaction with magnesium.
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    URL: http://dx.doi.org/10.1002/bip.360230707
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    Kinetics of irreversible dissociation for proteins bound cooperatively to DNA (1984)
    New York : Wiley-Blackwell
    Biopolymers 23 (1984), S. 1249-1259 
    Details
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: We consider the irreversible dissociation kinetics of proteins that bind cooperatively and nonspecifically to DNA. Our model consists of an infinitely long one-dimensional nucleic acid lattice on which are bound protein ligands. A set of adjacent bound proteins forms a cluster of length n. A protein molecule may dissociate from any site within the bound cluster, not only from the ends, as was assumed in a previous model of this process due to Lohman [(1983) Biopolymers 22, 1697-1713]. By considering this additional pathway, we present a more general treatment of the dissociation kinetics of cooperatively bound ligands. We show that dissociation from the (n-2) internal positions of an n-cluster is an important pathway when the initial fractional saturation of the lattice is close to unity and the co operatively is low. When the fractional saturation is initially equal to 1 and the co operatively is low, our model does not give the zero-order dissociation kinetics predicted by the Lohman model.
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    URL: http://dx.doi.org/10.1002/bip.360230709
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    Comments on the “ordinary-extraordinary phase transition” of poly(lysine) (1984)
    New York : Wiley-Blackwell
    Biopolymers 23 (1984), S. 1637-1646 
    Details
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The “ordinary-extraordinary phase transition” of poly(lysine), first reported by Lin et al. [(1978) Biopolymers 17, 1041-1064], has been reexamined as a function of the data collection interval (Δt) and scattering angle (θ). These data suggest that the relaxation domains “split” as the ionic strength is lowered through the transition region. In contrast, fluorescence photobleaching recovery data of Ware and coworkers (personal communication) indicate the tracer diffusion coefficient is not sensitive to the “ordinary-extraordinary phase transition.” The apparent discrepancy between these two techniques is here proposed to be due to small ion effects on both the dynamics and the scattering power of the polyelectrolytes.
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    URL: http://dx.doi.org/10.1002/bip.360230903
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    Counterion binding and hydration of hyaluronate and chondroitin in solution: An 17O, 23Na, and 25Mg nuclear-magnetic-relaxation study (1984)
    New York : Wiley-Blackwell
    Biopolymers 23 (1984), S. 1683-1699 
    Details
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Nuclear magnetic relaxation rates of H217O, 23Na+, and 25Mg2+ have been measured in aqueous hyaluronate solutions. The dependence on solution pH of the relaxation rates has been investigated, as well as the competition behavior of Na+ with Ca2+ and Mg2+. H217O and 23Na+ relaxation rates in chondroitin and hyaluronate solutions have been compared in the interval, 2 ≲ pH ≲ 12.5. The ion binding of hyaluronate can be fully accounted for by Coulomb interactions, with no need to involve chemical specificity. The hydration is only slighly pH dependent, and is comparable in magnitude to hydration of synthetic polyelectrolytes and monosaccharides. Ion-binding and hydration properties of hyaluronate and chondroitin are quite similar, except at elevated pH. At alkaline pH, an increase in charge density with pH is seen in hyaluronate and, to a much lesser degree, in chondroitin, possibly due to the titration of hydroxy groups. H217O data indicate an alkali-induced transition in both glycosaminoglycans.
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    URL: http://dx.doi.org/10.1002/bip.360230906
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    Dielectric properties of slightly hydrated collagen: Time-water content superposition analysis (1984)
    New York : Wiley-Blackwell
    Biopolymers 23 (1984), S. 1725-1734 
    Details
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The frequency dependences of the dielectric constant, ε′, and the loss factor, ε″, in collagen were measured at several water contents from 0.1 to 0.3 g/g collagen over a frequency range of 30 Hz to 100 kHz and at a temperature of 20°C. Remarkable dispersion was observed at the lower frequencies for higher water contents. According to accumulated results on the thermodynamic and structural investigations, the dispersion has some analogy to the surface conduction proposed by B. V. Hamon [(1953) Aust. J. Phys. 6, 304-315]. An empirical relation bewteen ε″ and frequency, f, ε″ ∝ fn, where 0 〈 n 〈 1, suggests that the dielectric and conductive properties of hydrated collagen are related to carrier jumps between neighboring sites. For the polarization mechanism of this dispersion, we supposed a model of the transfer of protons between absorbed water molecules, and found that the time-water content superposition procedure is applicable to slightly hydrated collagen. The results derived from the superposition procedure show that the water content, φ, is related to the conductivity, σ, or the dielectric loss factor by the following equations: σ (φ, f) = const. × φnm-1f1-n and ε″ (φ, f) = const. φnmf-n, respectively, where m is a constant independent of φ and f. These results agree with that derived by another treatment of the same data. The role of water molecules in the conduction and polarization in slightly hydrated collagen is considered to be not far from that assumed in the model.
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    URL: http://dx.doi.org/10.1002/bip.360230908
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    Thermodynamic stability of the ordered conformations of carrageenan polyelectrolytes (1984)
    New York : Wiley-Blackwell
    Biopolymers 23 (1984), S. 1771-1794 
    Details
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Manning's counterion condensation theory has been applied to the temperature-induced conformational transition of κ- and ι-carrageenan in the solution and gel states. The formalism of the theory has been extended to transitions between conformations with charge densities below or across the counterion condensation threshold. Measurements of the dependence of the melting temperature on ionic strength, and of the enthalpy of melting, are interpreted with the theory as indicating that the conformational transition is intramolecular and that side-by-side dimerization of chains gives rise to the gel structure.
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    URL: http://dx.doi.org/10.1002/bip.360230911
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    Azobenzene-Containing polypeptides: Photoregulation of conformation in solution (1984)
    New York : Wiley-Blackwell
    Biopolymers 23 (1984), S. 1423-1437 
    Details
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Photochromic polypeptides, with 16 to 56% azobenzene groups in the side chains, have been prepared by reaction of poly(L-glutamic acid) with p-aminozaobenzene, both in the presence of dicyclohexyl carbodiimide/N-hydroxybenzotriazole and of pivaloyl chloride. Analogous modification reactions carried out on poly(L-aspartic acid) were unsuccessful owing to the formation of N-succinimide rings. In trimethylphosphate, all the azopolypeptides exhibit the α-helix CD pattern. Irradiation produces the trans-to-cis isomerization of the azo side chains, but does not induce any variations of the backbone conformation. In water, the CD spectra indicate the presence of appreciable amounts of α helix in 16 and 21% mol azo-containing poly-(Lglutamates), while a β structure is present in a 36% mol azopolypeptide. Light produces conformational changes of the polypeptide conformation which are completely reversed in the dark. The extent and kind of photobehavior depend on the azo content and the pH value at which irradiation is carried out. The light-induced effects are discussed on the basis of the pH-induced order-disorder conformational transitions. In fact, the pK values and the transition curves of the dark-adapted samples were found to be different from those of the irradiated ones.
    Additional Material: 8 Ill.
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    URL: http://dx.doi.org/10.1002/bip.360230723
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    Vibrational circular dichroism of polypeptides. II. Solution amide II and deuteration results (1984)
    New York : Wiley-Blackwell
    Biopolymers 23 (1984), S. 1519-1532 
    Details
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Vibrational CD (VCD) of amide I and II vibrations of several α-helical polypeptides have been measured in solution. For the amide II as well as the amide I [previously published: Lal, B.B. & Nafie, L.A. (1982) Biopolymers 21, 2161] we find the VCD to be characteristic of the polypeptide secondary structure. Amide II bands of right-handed α helices were all found to have negative VCD and to have their maximum rotational strength for the parallel (low-energy) component. However, left-handed α helices formed from L-amino acids gave positive amide II bands at higher frequencies than found for the right-handed helices, indicating that the VCD was sensitive to the stereochemical difference. The amide-I VCD spectra of some deuterated right-handed α-helical polypeptides have a new negative feature to low frequency that does not reflect theoretical predictions but also appears to be stereochemically sensitive. Amide-II and amide-A VCD of a few deuterated polypeptides imply retention of the secondary-structure-dependent characteristics seen in the hydrogenated VCD.
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    URL: http://dx.doi.org/10.1002/bip.360230808
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    Vibrational circular dichroism of polypeptides. III. Film studies of several α-helical and β-sheet polypeptides (1984)
    New York : Wiley-Blackwell
    Biopolymers 23 (1984), S. 1533-1545 
    Details
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Vibrational CD (VCD) of amides A, I, and II vibrations of a variety of polypeptide films have been measured. VCD of films of α-helical and β-sheet structures are compared in the three regions. Reproducible spectra could only be obtained for thin films free of orientation dependence. The sign and band shape of the VCD of films are not always the same as that in solution. However, the magnitude of the observed VCD seems to correlate with the secondary structure such that α-helical molecules typically have much larger Δε/ε values than do β-sheet molecules. The possibility of interference by artifacts owing to light-scattering effects is discussed.
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    URL: http://dx.doi.org/10.1002/bip.360230809
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    Masthead (1984)
    New York : Wiley-Blackwell
    Biopolymers 23 (1984) 
    Details
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/bip.360230901
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